Prokaryote gene location report

Prokaryote gene location record identifiers, organism, and genomic locations

Prokaryote gene location report

Prokaryote gene location record identifiers, organism, and genomic locations

The downloaded prokaryote package contains a prokaryote gene location data report in JSON Lines format in the file:

ncbi_dataset/data/annotation_report.jsonl

Each line of the prokaryote gene location data report file is a hierarchical JSON object that represents a single prokaryote gene location record. The schema of the prokaryote gene location record is defined in the tables below where each row describes a single field in the report or a sub-structure, which is a collection of fields. The outermost structure of the report is ProkaryoteGeneLocation.

Table fields that include a Table Field Mnemonic can be used with the dataformat command-line tool's --fields option. Refer to the dataformat CLI tool reference to see how you can use this tool to transform prokaryote gene location data reports from JSON Lines to tabular formats.

Sample report

{
  "chromosomeName": "plasmid:p2017-45-35",
  "genbankGenomicLocation": {
    "assemblyAccession": "GCA_030179155.1",
    "sequenceRange": {
      "accessionVersion": "CP109734.1",
      "range": [
        {
          "begin": "37360",
          "end": "37773",
          "orientation": "minus"
        }
      ]
    }
  },
  "organism": {
    "organismName": "Providencia thailandensis",
    "strain": "2017-45-35",
    "taxId": 990144
  },
  "proteinAccession": "WP_001435165.1",
  "refseqGenomicLocation": {
    "assemblyAccession": "GCF_030179155.1",
    "sequenceRange": {
      "accessionVersion": "NZ_CP109734.1",
      "range": [
        {
          "begin": "37360",
          "end": "37773",
          "orientation": "minus"
        }
      ]
    }
  }
}

ProkaryoteGeneLocation Structure

Field	Table Field Mnemonic	Table Column Name	Type	Description	Examples
`proteinAccession`	`protein-accession`	Protein Accession	`string`	The RefSeq WP_ prefixed accession for the protein sequence.	`WP_000443665.1`
`refseqGenomicLocation`	`refseq-genomic-location-`	RefSeq Genomic Location	`SeqRangeWithAssembly`	The RefSeq nucleotide mapping for this protein
`genbankGenomicLocation`	`genbank-genomic-location-`	GenBank Genomic Location	`SeqRangeWithAssembly`	The equivalent GenBank nucleotide mapping for this protein
`organism`	`organism-`	Organism	`Organism`	The species level taxonomy information
`completeness`	`completeness`	Completeness	`ProkaryoteGeneLocation.Completeness`	Whether the assembly is complete or partial
`chromosomeName`	`chromosome_name`	Chromosome	`string`	The name of the chromosome, if there is one.

InfraspecificNames Structure

Field	Table Field Mnemonic	Table Column Name	Type	Description	Examples
`breed`	`breed`	Breed	`string`	A homogenous group of animals within a domesticated species	`Hereford` `boxer`
`cultivar`	`cultivar`	Cultivar	`string`	A variety of plant within a species produced and maintained by cultivation	`B73`
`ecotype`	`ecotype`	Ecotype	`string`	A population or subspecies occupying a distinct habitat	`Alpine`
`isolate`	`isolate`	Isolate	`string`	The individual isolate from which the sequences in the genome assembly were derived	`L1 Dominette 01449 registration number 42190680` `Pmale09`
`sex`	`sex`	Sex	`string`	Male or female	`female`
`strain`	`strain`	Strain	`string`	A genetic variant, subtype or culture within a species	`SE11`

LineageOrganism Structure

Field	Table Field Mnemonic	Table Column Name	Type	Description	Examples
`taxId`	coming soon	coming soon	`uint32`	NCBI Taxonomy identifier	`11118`
`name`	coming soon	coming soon	`string`	Scientific name	`Coronaviridae`

Organism Structure

Field	Table Field Mnemonic	Table Column Name	Type	Description	Examples
`taxId`	`tax-id`	Taxonomic ID	`uint32`	NCBI Taxonomy identifier	`9606` `2697049`
`organismName`	`name`	Name	`string`	Scientific name	`Homo sapiens` `Severe acute respiratory syndrome coronavirus 2`
`commonName`	`common-name`	Common Name	`string`	Common name	`human` `pangolin` `MERS` `SARS2`
`lineage repeated`			`LineageOrganism`	Lineage ordered from superkingdom level to increasingly more specific taxonomic entries
`pangolinClassification`	`pangolin`	Pangolin Classification	`string`		`B.1.1.7`
`infraspecificNames`	`infraspecific-`	Infraspecific Names	`InfraspecificNames`

Range Structure

A 1-based range on a sequence record.

Field	Table Field Mnemonic	Table Column Name	Type	Description
`begin`	`start`	Start	`uint64`
`end`	`stop`	Stop	`uint64`
`orientation`	`orientation`	Orientation	`Orientation`
`order`	`order`	Order	`uint32`
`ribosomalSlippage`	coming soon	coming soon	`int32`	When ribosomal slippage is desired, fill out slippage amount between this and previous range.

SeqRangeSet Structure

Field	Table Field Mnemonic	Table Column Name	Type	Description	Examples
`accessionVersion`	`accession`	Sequence Accession	`string`	NCBI Accession.version of the sequence
`range repeated`	`range-`		`Range`	Series of intervals on above accession_version

SeqRangeWithAssembly Structure

Field	Table Field Mnemonic	Table Column Name	Type	Description	Examples
`assemblyAccession`	`assembly-accession`	Assembly Accession	`string`	The genomic assembly associated with the sequence location of this protein	`GCF_000010385.1`
`sequenceRange`	`seq-range-`		`SeqRangeSet`	The genomic sequence location of this protein

Orientation Enumeration

Name	Number	Description
`none`	`0`
`plus`	`1`
`minus`	`2`

ProkaryoteGeneLocation.Completeness Enumeration

Name	Number	Description
`complete`	`0`
`partial`	`1`

Scalar Value Types

Protocol buffers type	Notes	C++	Python	Java	Go
`double`		`double`	`float`	`double`	`float64`
`float`		`float`	`float`	`float`	`float32`
`int32`	Uses variable-length encoding. Inefficient for encoding negative numbers – if your field is likely to have negative values, use sint32 instead.	`int32`	`int`	`int`	`int32`
`int64`	Uses variable-length encoding. Inefficient for encoding negative numbers – if your field is likely to have negative values, use sint64 instead.	`int64`	`int/long`	`long`	`int64`
`uint32`	Uses variable-length encoding.	`uint32`	`int/long`	`int`	`uint32`
`uint64`	Uses variable-length encoding.	`uint64`	`int/long`	`long`	`uint64`
`sint32`	Uses variable-length encoding. Signed int value. These more efficiently encode negative numbers than regular int32s.	`int32`	`int`	`int`	`int32`
`sint64`	Uses variable-length encoding. Signed int value. These more efficiently encode negative numbers than regular int64s.	`int64`	`int/long`	`long`	`int64`
`fixed32`	Always four bytes. More efficient than uint32 if values are often greater than 2^28.	`uint32`	`int`	`int`	`uint32`
`fixed64`	Always eight bytes. More efficient than uint64 if values are often greater than 2^56.	`uint64`	`int/long`	`long`	`uint64`
`sfixed32`	Always four bytes.	`int32`	`int`	`int`	`int32`
`sfixed64`	Always eight bytes.	`int64`	`int/long`	`long`	`int64`
`bool`		`bool`	`boolean`	`boolean`	`bool`
`string`	A string must always contain UTF-8 encoded or 7-bit ASCII text.	`string`	`str/unicode`	`String`	`string`
`bytes`	May contain any arbitrary sequence of bytes.	`string`	`str`	`ByteString`	`[]byte`

Generated May 16, 2024